A simple soil organic-matter model for biomass data assimilation in community-level carbon contracts

Soil carbon (C) sequestration has been proposed as a transitional win-win strategy to help replenish organic-matter content in depleted agricultural soils and counter increases in atmospheric greenhouse gases. Data assimilation and remote sensing can reduce uncertainty in sequestered C mass estimates, but simple soil organic carbon (SOC) models are required to make operational predictions of tradeable amounts over large, heterogenous areas. Our study compared the performance of RothC26.3 and a reduced compartmental model on an 11-year fertilizer trial in subhumid West Africa. Root mean square error (RMSE) differences of 0.05 Mg C/ha between models on total SOC predictions suggest that for contractual purposes, SOC dynamics can be simulated by a two-pool structure with labile and stable components. Faster (seasonal) and slower (semicentennial and beyond) rates can be approximated by constants as instantaneous and infinite decay. In these systems, simulations indicate that cereal residue incorporation holds most potential for mitigation of transient C loss associated with recent land conversion to agriculture

Perennial grain crops in the West Soudanian Savanna of Mali: perspectives from agroecology and gendered spaces

Perennial grain crops may play an important role in environmentally sound and socially just food systems for Africa. We study the future possibility of integrating perennial grains into Malian farming systems from the perspective of agroecology, and more specifically using a gendered space approach. We interviewed 72 farmers across the sorghum-growing region of Mali. We found that perennial grains offer a vision for transforming human relations with nature that mirrors the resource sharing of customary land tenure, including patterns of extensive and intensive land use in time and space. Women interviewees identified a broad set of potential advantages and challenges to perennial grain production. Advantages include reduced labour, saving seed, and improving food security. Women farmers were concerned about livestock, water access, and resource limitations. We argue that perennial grains may increase access to land and natural resources for women farmers. Perennial grains may improve soil quality, reduce labour early in the rainy season, and provision more resources from fallow lands. Pastoralists stand to benefit from improved pastures in the dry season. We conclude that investments are needed to develop viable crop types in consideration of the complexity of West African farming systems and the local needs of women farmers and pastoralists

Canadian Experiment for Soil Moisture in 2010 (CanEX-SM10): Overview and Preliminary Results

The Canadian Experiment for Soil Moisture in 2010 (CanEx-SM10) was carried out in Saskatchewan, Canada from 31 May to 16 June, 2010. Its main objective was to contribute to Soil Moisture and Ocean salinity (SMOS) mission validation and the pre-launch assessment of Soil Moisture and Active and Passive (SMAP) mission. During CanEx-SM10, SMOS data as well as other passive and active microwave measurements were collected by both airborne and satellite platforms. Ground-based measurements of soil (moisture, temperature, roughness, bulk density) and vegetation characteristics (Leaf Area Index, biomass, vegetation height) were conducted close in time to the airborne and satellite acquisitions. Besides, two ground-based in situ networks provided continuous measurements of meteorological conditions and soil moisture and soil temperature profiles. Two sites, each covering 33 km x 71 km (about two SMOS pixels) were selected in agricultural and boreal forested areas in order to provide contrasting soil and vegetation conditions. This paper describes the measurement strategy, provides an overview of the data sets and presents preliminary results. Over the agricultural area, the airborne L-band brightness temperatures matched up well with the SMOS data. The Radio frequency interference (RFI) observed in both SMOS and the airborne L-band radiometer data exhibited spatial and temporal variability and polarization dependency. The temporal evolution of SMOS soil moisture product matched that observed with the ground data, but the absolute soil moisture estimates did not meet the accuracy requirements (0.04 m3/m3) of the SMOS mission. AMSR-E soil moisture estimates are more closely correlated with measured soil moisture

Tuberculosis drug resistance in Bamako, Mali, from 2006 to 2014.

BACKGROUND: Although Drug resistance tuberculosis is not a new phenomenon, Mali remains one of the "blank" countries without systematic data. METHODS: Between 2006 and 2014, we enrolled pulmonary TB patients from local TB diagnostics centers and a university referral hospital in several observational cohort studies. These consecutive patients had first line drug susceptibility testing (DST) performed on their isolates. A subset of MDR was subsequently tested for second line drug resistance. RESULTS: A total of 1186 mycobacterial cultures were performed on samples from 522 patients, including 1105 sputa and 81 blood samples, yielding one or more Mycobacterium tuberculosis complex (Mtbc) positive cultures for 343 patients. Phenotypic DST was performed on 337 (98.3%) unique Mtbc isolates, of which 127 (37.7%) were resistant to at least one drug, including 75 (22.3%) with multidrug resistance (MDR). The overall prevalence of MDR-TB was 3.4% among new patients and 66.3% among retreatment patients. Second line DST was available for 38 (50.7%) of MDR patients and seven (18.4%) had resistance to either fluoroquinolones or second-line injectable drugs. CONCLUSION: The drug resistance levels, including MDR, found in this study are relatively high, likely related to the selected referral population. While worrisome, the numbers remained stable over the study period. These findings prompt a nationwide drug resistance survey, as well as continuous surveillance of all retreatment patients, which will provide more accurate results on countrywide drug resistance rates and ensure that MDR patients access appropriate second line treatment

Implementing Preventive Chemotherapy through an Integrated National Neglected Tropical Disease Control Program in Mali

Neglected tropical diseases (NTDs) are a group of chronic infections that affect the poorest group of the populations in the world. There are currently five major NTDs targeted through mass drug treatment in the affected communities. The drug delivery can be integrated to deliver different drug packages as these NTDs often overlap in distribution. Mali is endemic with all five major NTDs. The integrated national NTD control program was implemented through the primary health care system using the community health center workers and the community drug distributors aiming at long-term sustainability. After a pilot start in three regions in 2007 without prior examples to follow on integrated mass drug administration, treatment for the five targeted NTDs was gradually scaled up and reached all endemic districts by 2009, and annual drug coverage in the targeted population has since been maintained at a high level for each of the five NTDs. Around 10 million people received one or more drug treatments each year since 2009. The country is on the way to meet the national objectives of elimination or control of these diseases. The successes and lessons learned in Mali are valuable assets to other countries looking to start similar programs

Failure to Recognize Nontuberculous Mycobacteria Leads to Misdiagnosis of Chronic Pulmonary Tuberculosis

BACKGROUND: Nontuberculous mycobacterial (NTM) infections cause morbidity worldwide. They are difficult to diagnose in resource-limited regions, and most patients receive empiric treatment for tuberculosis (TB). Our objective here is to evaluate the potential impact of NTM diseases among patients treated presumptively for tuberculosis in Mali. METHODS: We re-evaluated sputum specimens among patients newly diagnosed with TB (naïve) and those previously treated for TB disease (chronic cases). Sputum microscopy, culture and Mycobacterium tuberculosis drug susceptibility testing were performed. Identification of strains was performed using molecular probes or sequencing of secA1 and/or 16S rRNA genes. RESULTS: Of 142 patients enrolled, 61 (43%) were clinically classified as chronic cases and 17 (12%) were infected with NTM. Eleven of the 142 (8%) patients had NTM disease alone (8 M. avium, 2 M. simiae and 1 M. palustre). All these 11 were from the chronic TB group, comprising 11/61 (18%) of that group and all were identified as candidates for second line treatment. The remaining 6/17 (35.30%) NTM infected patients had coinfection with M. tuberculosis and all 6 were from the TB treatment naïve group. These 6 were candidates for the standard first line treatment regimen of TB. M. avium was identified in 11 of the 142 (8%) patients, only 3/11 (27.27%) of whom were HIV positive. CONCLUSIONS: NTM infections should be considered a cause of morbidity in TB endemic environments especially when managing chronic TB cases to limit morbidity and provide appropriate treatment

Feasibility of Onchocerciasis Elimination with Ivermectin Treatment in Endemic Foci in Africa: First Evidence from Studies in Mali and Senegal

The control of onchocerciasis, or river blindness, is based on annual or six-monthly ivermectin treatment of populations at risk. This has been effective in controlling the disease as a public health problem, but it is not known whether it can also eliminate infection and transmission to the extent that treatment can be safely stopped. Many doubt that this is feasible in Africa. A study was undertaken in three hyperendemic onchocerciasis foci in Mali and Senegal where treatment has been given for 15 to 17 years. The results showed that only few infections remained in the human population and that transmission levels were everywhere below postulated thresholds for elimination. Treatment was subsequently stopped in test areas in each focus, and follow-up evaluations did not detect any recrudescence of infection or transmission. Hence, the study has provided the first evidence that onchocerciasis elimination is feasible with ivermectin treatment in some endemic foci in Africa. Although further studies are needed to determine to what extent these findings can be extrapolated to other areas in Africa, the principle of onchocerciasis elimination with ivermectin treatment has been established

First Detection of Leishmania major DNA in Sergentomyia (Spelaeomyia) darlingi from Cutaneous Leishmaniasis Foci in Mali

Leishmania major complex is the main causative agent of zoonotic cutaneous leishmaniasis (ZCL) in the Old World. Phlebotomus papatasi and Phlebotomus duboscqi are recognized vectors of L. major complex in Northern and Southern Sahara, respectively. In Mali, ZCL due to L. major is an emerging public health problem, with several cases reported from different parts of the country. The main objective of the present study was to identify the vectors of Leishmania major in the Bandiagara area, in Mali. Methodology/Principal Findings: An entomological survey was carried out in the ZCL foci of Bandiagara area. Sandflies were collected using CDC miniature light traps and sticky papers. In the field, live female Phlebotomine sandflies were identified and examined for the presence of promastigotes. The remaining sandflies were identified morphologically and tested for Leishmania by PCR in the ITS2 gene. The source of blood meal of the engorged females was determined using the cyt-b sequence. Out of the 3,259 collected sandflies, 1,324 were identified morphologically, and consisted of 20 species, of which four belonged to the genus Phlebotomus and 16 to the genus Sergentomyia. Leishmania major DNA was detected by PCR in 7 of the 446 females (1.6%), specifically 2 out of 115 Phlebotomus duboscqi specimens, and 5 from 198 Sergentomyia darlingi specimens. Human DNA was detected in one blood-fed female S. darlingi positive for L. major DNA. Conclusion: Our data suggest the possible involvement of P. duboscqi and potentially S. darlingi in the transmission of ZCL in Mali

Temporal dynamic of malaria in a suburban area along the Niger River

Background: Even if rainfall and temperature are factors classically associated to malaria, little is known about other meteorological factors, their variability and combinations related to malaria, in association with river height variations. Furthermore, in suburban area, urbanization and growing population density should be assessed in relation to these environmental factors. The aim of this study was to assess the impact of combined environmental, meteorological and hydrological factors on malaria incidence through time in the context of urbanization. Methods: Population observational data were prospectively collected. Clinical malaria was defined as the presence of parasites in addition to clinical symptoms. Meteorological and hydrological factors were measured daily. For each factors variation indices were estimated. Urbanization was yearly estimated assessing satellite imaging and field investigations. Principal component analysis was used for dimension reduction and factors combination. Lags between malaria incidences and the main components were assessed by cross-correlation functions. Generalized additive model was used to assess relative impact of different environmental components, taking into account lags, and modelling non-linear relationships. Change-point analysis was used to determine transmission periods within years. Results: Malaria incidences were dominated by annual periodicity and varied through time without modification of the dynamic, with no impact of the urbanization. The main meteorological factor associated with malaria was a combination of evaporation, humidity and rainfall, with a lag of 3 months. The relationship between combined temperature factors showed a linear impact until reaching high temperatures limiting malaria incidence, with a lag 3.25 months. Height and variation of the river were related to malaria incidence (respectively 6 week lag and no lag). Conclusions: The study emphasizes no decreasing trend of malaria incidence despite accurate access to care and control strategies in accordance to international recommendations. Furthermore, no decreasing trend was showed despite the urbanization of the area. Malaria transmission remain increase 3 months after the beginning of the dry season. Addition to evaporation versus humidity/rainfall, nonlinear relationship for temperature and river height and variations have to be taken into account when implementing malaria control programmes